High density arrays such as microarrays are well-known and widely used to generate information about biological systems. Analysis of the data obtained from such arrays may be used in the development of new drugs and new diagnostic tools. However, the analysis of such data may be quite complex. In many such systems there are multiple sources of experimental error in the system. One way to reduce errors is to use replicate arrays in an experiment. However, even with replicate arrays it may be difficult to discern whether differences shown in the microarray data sets are genuine. Hence there is a need in the art for improved methods, systems, and products to reliably identify true positives in microarray-based experiments. The present invention meets these and other needs in the art,